9/23/12 nanoMATERIALS simulaon tool First-7me-user guide Strachan Group School of Materials Engineering and Birck nanotechnology Center Purdue University [email protected] nanoMATERIALS simulaon tool This tool allows users to perform molecular dynamics simulaons of metals and semiconductor structures. Proper7es and processes that can be studied include thermo-mechanical proper7es and thermal transport Addi$on informa$on • Topics page on MD simulaons: hQp://nanohub.org/topics/MD • Lecture series on MD simulaons of materials: hQp://nanohub.org/resources/5838 • Publicaons: “Molecular Dynamics Simulaons of Strain Engineering and Thermal Transport in Nanostructured Materials”, Y. Park, Y. Zhou, J. Jhaveri, and A. Strachan, Compu7ng In Science & Engineering 12 36-42 (2010). 1 9/23/12 Go to nanohub.org Click here to Register Register an Account Complete all required fields and submit. A conformaon email will be sent. 2 9/23/12 Login The link in the conformaon email will direct you to the login screen My HUB Logging in will bring you to the “My HUB” page. Here you can view recently opened tools and any open sessions. 3 9/23/12 The Tool URL Once you are logged in enter the URL for the tool as seen above. Launching the Tool Click here to open a session for this tool 4 9/23/12 nano-materials Toolkit The specifics of each simulaon will be determined by the informaon entered on these tabs Note the scroll bar When all necessary fields are completed, this buQon will begin simulaon This buQon will open the tool in a separate window if desired My HUB Access Now that you have accessed the tool, it is available from your “My HUB” page. If you accidentally close the browser window or leave the website, your tool session will remain open. It can be accessed here. New sessions of the nano- Materials Simulaon Toolkit can now be opened in the recent tools tab. 5 9/23/12 Input Model Tab The atomic model to be used. This is a Planum (100) cell. These values are the number of 7mes that the unit cell is repeated in the model. This will produce a 10x10x10 unit cell structure. Leave this checkbox as “no” and the Translate Atoms values as “0”. Energy Expression Tab This is the model by which the atomic interac7ons will be calculated. We use EAM (Embedded Atom Model). nanoMATERIALS uses Embedded Atom Model (EAM) poten7als for metals and Sllinger-Weber for Si. 6 9/23/12 Driver Specificaon Tab This is the 7me step (∆t). This simulaon will be in .004 ps increments. The number of total 7me steps. The simulated temperature. The amount of strain placed on each axis per 7me step. These values represent the number of steps between recorded values. For example, out of the 3000 total 7me steps, the trajectory data will be recorded six 7mes: once Thermalizaon simulates the random mo7on of every 500 steps. atoms for a specific number of 7me steps before deformaon begins. Leave the box unchecked “no”. Advanced Op7ons Tab The “Advanced Script” region is where any extra commands will be wriQen in code. Lines beginning with a “#” are comment lines. They will be ignored as the program runs. These lines are already present when you load the tool and give some instruc7ons for addi7onal code. The following slides provide examples of how to create nanostructures using the advanced op7ons tab 7 9/23/12 Advanced Op7ons: creang a sphere Step 1. Create a Pt 10x10x10 supercell. Simulaon cell length: 10xa0=3.95 nm Step 2. Select a sphere of desired radius, invert selec7on (select all atoms outside sphere) and delete selected atoms In Advanced Tab: Note: to avoid spheres from interac7ng with periodic images the simulaons cell length should be larger than the radius diameter + poten7al cutoff distance Advanced Op7ons: creang a nanowire between slabs 1 - The first line selects all atoms in the 4 – The fourth line inverts the en7re supercell from a height of 11.575 to a selec7on. This will result in a ring shape. height of 27.27 5 – The fiph line deletes all selected atoms 2 – The second line inverts that leaving just the nanowire with a substrate selecon. on top and boQom. 3 - The third line selects a cylinder of radius 11.875 centered at (19.625,19.625). 1 This is in addi7on to the selec7on from 2. 2 3 4 Unselected Selected 5 0 - 10x10 Cell 1 2 3 4 5 8 9/23/12 Simulate Aper all variables and code is entered correctly, click “Simulate” in the boQom right corner of the tool. The tool will now run the code. Data will be calculated and displayed on the screen. This can take several minutes depending on the size/type of the supercell and the number of 7me steps. Clicking “Abort” will halt the simulaon. Output Drop down menu for each result. Click Structure to view the structure snapshots at various 7mes throughout the test. To go back and try different parameters click “Input”. Aper mul7ple tests in the same session, this slider will appear allowing you to go back to previous results. Changes from test to test are indicated in the light blue area. 9 9/23/12 Structure Results Holding the lep mouse buQon anywhere on the image will allow you to manipulate the view. This buon will bring you back to the original view. This will change from a perspec7ve projec7on to an orthoscopic projecon. Give it a try. Orthoscopic vs. Perspecve Projecons Orthoscopic Perspecve 10 9/23/12 Comparing Structures at Different Times Structure at 2.0 ps Structure at 10.0 ps Expor7ng an Image Once you are sasfied with your image, click here to save. Make sure “Image File” is selected and click “Download”. You may have to set your browser to allow pop-ups from nanohub.org and try again. A new browser window will pop up and allow you to save the .png image file. 11 .